As Egypt lurches into a new era, a look at its complexities and subtleties helps us to understand the country’s likely course. Some thoughts on key issues:

The spirit of Tahrir Square is real and alive but exceedingly remote from the halls of power. Revolutionary ideas — that government should serve the people, not the reverse; that rulers should be chosen by the people; and that individuals have inherent dignity and rights — have finally penetrated a substantial portion of the country, and especially the young. In the long term, these ideas can work wonders. But for now, they are dissident ideas, firmly excluded from any operational role.

Military rule will continue. Soldiers did not seize power with Hosni Mubarak’s departure two months ago; they did so in 1952. That’s when the Free Officers overthrew the constitutional monarchy and took control. One senior military man has followed another — from Naguib to Nasser to Sadat to Mubarak to Tantawi — in an unbroken succession over 59 years. With time, the military expanded its grip from the political realm to the economic, producing everything from television sets to olive oil and acquiring control over a sizable portion of Egypt’s wealth. The soldiers have become far too accustomed to power and the good life to give up these perks. They will do whatever it takes, be it purging Mubarak, throwing his sons in jail, banning his old political party, changing the constitution, or repressing dissent, to keep power.

The military is not secular. From the furthest origins of the Free Officers in the 1930s to the recent reaffirmation of Sharia (Islamic law) as “the principal source of legislation,” the Egyptian military leadership consistently has displayed an Islamist orientation. More specifically, the Free Officers emerged out of the military wing of the Muslim Brotherhood and through the decades has been in competition with the civilian wing. As analyst Cynthia Farahat writes in the Middle East Quarterly, their rivalry “should be understood not as a struggle between an autocratic, secular dictatorship and a would-be Islamist one but a struggle between two ideologically similar, if not identical, rival groups, hailing from the same source.”

The Muslim Brotherhood is not a powerhouse. The organization suffers from major problems. First, hot-headed and violent Islamists despise it. Al-Qaeda recently blasted it for taking part in elections and ridiculed it for being on the path to becoming “secular and falsely affiliated with Islam.” Second, the brotherhood is weak on the ground. Hesham Kassem of the Egyptian Organization for Human Rights notes that its membership does not exceed 100,000 people, which, in a country of 80 million, means it “is not really a grass roots movement,” but a coddled institution benefiting from being uniquely tolerated. Genuine political competition should diminish its appeal.

Finally, understanding Egyptian politics means penetrating the characteristically Middle Eastern double game (as in Iraqi and Syrian politics), one played out here by the military and the Islamdfists. On the one hand, we see routine cooperation between the military and Islamists, and on the other hand, we see the military government exploiting fears of the Muslim Brotherhood.

Routine military–Islamist cooperation. The military has, Farahat notes, “subtly colluded with Islamists against their more democratically inclined compatriots and religious minorities, notably the Copts.” One of many examples: On April 14, a human-rights conference critiquing the military for hauling civilians before military tribunals was twice interrupted, first by a military police officer worried about “indecent women” and second by Islamists angry about inappropriate discussion of the military. Who is who? Roles have become nearly interchangeable. Likewise, the new military leadership permitted Islamists to form political parties and releasedbrotherhood members from jail. Conversely, Mohamed Badei, the brotherhood’s leader, praised the armed forces, and his organization endorsed the army’s March referendum.

The government exploits fears of the Muslim Brotherhood. The military benefits from worries, both domestic and foreign, of an Islamist takeover. That prospect justifies not only its own continued domination of Egypt but also excuses its excesses and cruelties. The military has learned to play Islamists like a yo-yo. For example, Mubarak cunningly allowed 88 Muslim Brothers into parliament in 2005; this simultaneously showed the perils of democracy and made his own tyranny indispensible. Having established this point, he allowed just one Muslim Brother into parliament in the 2010 elections.

In brief, while the modernity of Tahrir Square and the barbarism of the Muslim Brotherhood both have long-term importance, in all likelihood, the military will continue to rule Egypt, making only cosmetic changes.